RNA-Seq Data Mining: Downregulation of NeuroD6 Serves as a Possible Biomarker for Alzheimer’s Disease Brains

Alzheimer’s disease (AD) is the most common cause of dementia worldwide with no curative therapies currently available. Previously, global transcriptome analysis of AD brains by microarray failed to identify the set of consistently deregulated genes for biomarker development of AD. Therefore, the mo...

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Bibliographic Details
Published in:Disease markers Vol. 2014; no. 2014; pp. 1 - 10
Main Authors: Kitano, Shouta, Asahina, Naohiro, Yamamoto, Yoji, Satoh, J.-I., Kino, Yoshihiro
Format: Journal Article
Language:English
Published: Cairo, Egypt Hindawi Publishing Corporation 01.01.2014
John Wiley & Sons, Inc
Subjects:
Aged
Aged, 80 and over
Alzheimer Disease - metabolism
Alzheimer's disease
Basic Helix-Loop-Helix Transcription Factors - genetics
Basic Helix-Loop-Helix Transcription Factors - metabolism
Biological markers
Biomarkers - metabolism
Brain
Cerebral Cortex - metabolism
Diagnosis
Down-Regulation
Female
Humans
Male
Medical research
Medicine, Experimental
Middle Aged
Physiological aspects
Sequence Analysis, RNA
Transcriptome
ISSN:0278-0240, 1875-8630, 1875-8630
Online Access:Get full text
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Summary:Alzheimer’s disease (AD) is the most common cause of dementia worldwide with no curative therapies currently available. Previously, global transcriptome analysis of AD brains by microarray failed to identify the set of consistently deregulated genes for biomarker development of AD. Therefore, the molecular pathogenesis of AD remains largely unknown. Whole RNA sequencing (RNA-Seq) is an innovative technology for the comprehensive transcriptome profiling on a genome-wide scale that overcomes several drawbacks of the microarray-based approach. To identify biomarker genes for AD, we analyzed a RNA-Seq dataset composed of the comprehensive transcriptome of autopsized AD brains derived from two independent cohorts. We identified the core set of 522 genes deregulated in AD brains shared between both, compared with normal control subjects. They included downregulation of neuronal differentiation 6 (NeuroD6), a basic helix-loop-helix (bHLH) transcription factor involved in neuronal development, differentiation, and survival in AD brains of both cohorts. We verified the results of RNA-Seq by analyzing three microarray datasets of AD brains different in brain regions, ethnicities, and microarray platforms. Thus, both RNA-Seq and microarray data analysis indicated consistent downregulation of NeuroD6 in AD brains. These results suggested that downregulation of NeuroD6 serves as a possible biomarker for AD brains.
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Academic Editor: Lance A. Liotta
ISSN:0278-0240
1875-8630
1875-8630
DOI:10.1155/2014/123165